These firms have nearly 70 million of the 900 million Indian subscribers.
February’s judgement said that they would need to transfer to other operators within the next four months.
However, the court agreed to hear a petition by the government seeking clarification on its judgement.
The government has told the court that more than 69 million mobile phone subscribers – 7.5% of total subscribers – could face service disruption as a fresh auction of the licences was not possible by 2 June, the deadline set by the court.
The licences were issued by former minister A Raja, who is accused of mis-selling bandwidth in what has been called India’s biggest corruption scandal. Mr Raja, who is currently on trial for fraud, denies wrongdoing.
Government auditors say the scandal cost the country about $40bn (£24.5bn).
On Wednesday, the court rejected the petitions of seven telecommunications companies seeking a review of the judgement and said: “We have carefully perused the record of the case and are satisfied that the judgment of which review has been sought does not suffer from any error apparent.”